WB doesn't see them as the wrong characters. For WB, these games are a merchandising opportunity. They bought NRS/Midway and its intellectual property, and use the popularity of that property to promote other intellectual properties they want to promote for their film arm -- like Freddy (who had a reboot coming after MK9), Jason (whose reboot was ultimately cancelled), Alien vs Predator (Alien: Covenant and other franchise developments in the works), Leatherface (reboot coming this year), and now Hellboy with his reboot film coming next year.
Nevermind that Hellboy is actually a pretty great choice for a comic book fighting game as a guest character, as he's one of the most popular comic characters around that isn't a DC or Marvel property.
WB is doing exactly what they want to be doing promotionally, and from their perspective it's a success. It means the roster isn't what we as hardcore fans of MK or the DC universe want, but that isn't their priority necessarily.
Personally I was really upset by all the guest characters in MKX, but to say WB isn't professional or doing exactly what they should be doing for their bottom line is silly. They're out for themselves, not for NRS. NRS is a vehicle for them, and one that they finance.